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The big benefit to at least HAVING the ePub version available to you is the fact YOU have a copy of it, and are thus protected from (heaven forbid) Kobo going out of business and the infrastructure to download and sync kepub's ceases to exist.
Some folks also like the fact that they can "tweak" ePubs to remove their dislikes in formatting.
Also if you are a multiple Kobo family (for instance Taming here), all the readers are registered to the same account, and thus if both people read the same book, the Kobo syncing of reading location within an kePub would become annoying.
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